A Compendium of Cyanobacterial Genomes and Proteomes

RESEARCH ARTICLE Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and Proteomes

Arul Prakasam Peter1☯, Karthick Lakshmanan1☯, Shylajanaciyar Mohandass1, Sangeetha Varadharaj1, Sivasudha Thilagar2, Kaleel Ahamed Abdul Kareem3, Prabaharan Dharmar1, Subramanian Gopalakrishnan1, Uma Lakshmanan1*

1 National Facility for Marine Cyanobacteria, Sub-Distributed Bioinformatics Centre (sponsored by Department of Biotechnology, Govt. of India), Department of Marine Biotechnology, School of Marine a11111 Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India, 2 Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India, 3 Department of Botany, Jamal Mohammed College, Tiruchirappalli, Tamil Nadu, India

☯ These authors contributed equally to this work. * [email protected]

OPEN ACCESS

Citation: Peter AP, Lakshmanan K, Mohandass S, Abstract Varadharaj S, Thilagar S, Abdul Kareem KA, et al. Cyanobacterial KnowledgeBase (CKB) is a free access database that contains the genomic (2015) Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to Proteomes. PLoS ONE 10(8): e0136262. seven orders. The database also contains tools for sequence analysis. The Species report doi:10.1371/journal.pone.0136262 and the gene report provide details about each species and gene (including sequence fea- Editor: Christian Schönbach, Nazarbayev University, tures and gene ontology annotations) respectively. The database also includes cyano- KAZAKHSTAN BLAST, an advanced tool that facilitates comparative analysis, among cyanobacterial Received: November 5, 2014 genomes and genomes of E. coli (prokaryote) and Arabidopsis (eukaryote). The database

Accepted: August 3, 2015 is developed and maintained by the Sub-Distributed Informatics Centre (sponsored by the Department of Biotechnology, Govt. of India) of the National Facility for Marine Cyanobacte- Published: August 25, 2015 ria, a facility dedicated to marine cyanobacterial research. CKB is freely available at http:// Copyright: © 2015 Peter et al. This is an open nfmc.res.in/ckb/index.html. access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability Statement: The data used for this database is retrieved from the NCBI (ftp://ftp.ncbi.nih. gov/genomes/Bacteria/) and UniProt (http://www. Introduction uniprot.org/) repositories for the listed organisms and Cyanobacteria comprise over 1,600 species with various morphologies and species-specific there are no legal or ethical restrictions on usage of characteristics, such as cell movement, cell differentiation, and nitrogen fixation [1]. These are this data. The raw data downloaded from NCBI and UniProt repositories is formatted as per the CKB the only known oxygenic photosynthetic prokaryotic organisms that inhabit a wide range of database requirement. List of the accession numbers ecological habitats (e.g., extreme cold, extreme hot, marine, fresh water, and terrestrial) and used is uploaded as Supporting Information. exhibit symbiotic associations with other living organisms. These primitive oxygenic Gram

Funding: The authors thank the facility BT/03/040/89 negative bacteria are widely used as a valuable model to study the mechanism of carbon fixa- and the Sub-DIC (BT/BI/)4/038/02 for their fiscal tion and helpful for evolutionary biologists to understand the endosymbiotic theory, as they support. are considered as the origin of chloroplast. Since these ancient life forms play a major role in

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Competing Interests: The authors have declared many biogeochemical cycles of the global ecological system, they serve as a study material in that no competing interests exist. diverse fields of life-science research [2]. Cyanobacteria are well-known for the formation of toxic cyanobacterial water blooms in freshwater, brackish and coastal marine ecosystems, which are of vital ecological and human health concerns [3]. However, in recent times, these organisms have captured the attention of the researchers worldwide because of their capability of producing prolific bioactive natural products as secondary metabolites, which are of great economic and medical value [4–6]. The National Facility for Marine Cyanobacteria (Sponsored by the Department of Biotech- nology, Govt. of India) is dedicated to cyanobacterial research, especially marine cyanobacteria. One of the principal foci of the facility is to build a dedicated knowledge base for cyanobacteria. The increasing number of completely sequenced cyanobacterial genomes provides wide oppor- tunities for understanding the metabolic organization of the cyanobacterial species in diverse environments. Here we introduce the Cyanobacterial KnowldegeBase (CKB), a freely accessible, comprehensive database resource covering information pertaining to 74 completely sequenced cyanobacterial species. The database also includes an informative tool called cyano- BLAST, which helps in comparative analysis between cyanobacterial genomes and the genomes of pro- and eu-karyote, such as E. coli and Arabidopsis.

Results and Discussion Organisms Seventy-four fully sequenced genomes of seven orders are currently included in the CKB database. This comprises 12 species of Chroococcales, 1 of Chroococcidiopsidales, 2 of Gloeobac- teriales, 12 of Nostocales, 7 of Oscillatoriales, 2 of Pleurocapsales and 38 of Synechococcales. The web user interface of CKB is shown in (Fig 1) and the complete list of the species exists in the CKB is given in Table 1.

Tools The database analysis portal provides access to the CKB BLAST tool, as well as tools for pattern and fuzzy searches, and restriction digestion. The CKB BLAST tool can be used to compare nucleotide or protein sequences, to identify members of gene families, and to infer functional and evolutionary relationships between sequences. Users are provided with several customized databases for similarity searches within the CKB BLAST analysis tool. This includes a database with information on all cyanobacterial

Fig 1. CKB web interface. doi:10.1371/journal.pone.0136262.g001

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Table 1. Order wise complete list of species mentioned in CKB. The table provides information related to order, Morphology (Morph.-U: Unicellular, F: Filamentous and F,H: Filamentous Heterocystous), number of chromosomes (Chr.), number of plasmids (Pla.), genome size (Size, MB), GC %, the number of genes (Genes), number of proteins (Proteins), and Biological Resource Centers (BRCs) from which live specimens can be available for each species.

Order Organism Morph. Chr. Pla. Size, MB GC % Genes Proteins BRCs Chroococcales Cyanobacterium aponinum PCC 10605 U 1 0 4.72 60.5 4562 4507 PCC Cyanobacterium stanieri PCC 7202 U 1 0 4.66 62 4482 4430 PCC Cyanothece sp. ATCC 51142 U 1 6 7.06 38.8 6258 5838 ATCC Cyanothece sp. PCC 7424 U 2 3 5.31 38.1 4797 4511 PCC Cyanothece sp. PCC 7425 U 2 3 7.11 41.4 5813 5710 ATCC; PCC Cyanothece sp. PCC 7822 U 1 3 6.96 39.8 5841 5535 PCC Cyanothece sp. PCC 8801 U 1 0 7.02 42.2 6250 5950 PCC Cyanothece sp. PCC 8802 U 1 3 7.61 42.2 6738 6229 PCC Dactylococcopsis salina PCC 8305 U 1 2 5.49 38.3 5380 3651 PCC Gloeocapsa sp. PCC 7428 U 1 5 9.06 41.3 7164 6689 ATCC; PCC Halothece sp. PCC 7418 U 1 0 6.33 40.4 5538 5237 PCC Microcystis aeruginosa NIES-843 U 1 6 7.21 41.2 6213 6129 NIES Chroococcidiopsidales Chroococcidiopsis thermalis PCC 7203 U 1 2 6.72 41.5 5687 5449 ATCC; PCC Gloeobacteriales Gloeobacter kilaueensis JS1 U 1 2 8.73 37.5 6946 6644 NA Gloeobacter violaceus PCC 7421 U 1 9 8.36 47 8571 8383 ATCC; PCC Nostocales Anabaena cylindrica PCC 7122 F, H 1 0 6.79 44.3 6676 6630 ATCC; PCC Anabaena sp. 90 F, H 1 2 6.76 45.6 6426 5945 NA Anabaena variabilis ATCC 29413 F, H 1 8 5.62 40.2 5059 4752 ATCC Calothrix sp. PCC 630 F, H 1 1 4.18 35 3614 3431 ATCC; PCC Calothrix sp. PCC 7507 F, H 1 0 3.16 38.7 2941 2837 ATCC; PCC Cylindrospermum stagnale PCC 7417 F, H 1 0 3.34 68.7 3437 3280 ATCC; PCC Nostoc azollae 0708 F, H 2 4 5.46 38 5364 5303 NA Nostoc punctiforme PCC 73102 F, H 1 6 6.55 38.5 5942 5710 ATCC; PCC Nostoc sp. PCC 7107 F, H 1 3 5.79 50.7 5507 5327 ATCC; PCC Nostoc sp. PCC 7120 F, H 1 6 7.84 39.9 7042 6642 ATCC; PCC Nostoc sp. PCC 7524 F, H 1 3 4.79 39.8 4619 4367 ATCC; PCC Rivularia sp. PCC 7116 F, H 1 4 4.8 39.8 4700 4444 PCC Oscillatoriales Arthrospira platensis NIES-39 F 1 0 3.78 42.4 3684 3337 NIES Crinalium epipsammum PCC 9333 F 1 0 4.68 58.5 3912 3815 PCC Geitlerinema sp. PCC 7407 F 1 4 5.88 43.4 5304 5011 ATCC; PCC Microcoleus sp. PCC 7113 F 1 0 4.18 42.9 3920 3708 PCC Oscillatoria acuminata PCC 6304 F 1 0 5.13 43.9 4654 4228 ATCC; PCC Oscillatoria nigro-viridis PCC 7112 F 1 8 7.97 46.2 6821 6441 PCC Trichodesmium erythraeum IMS101 F 1 0 5.84 42.3 6364 6312 NCMA Pleurocapsales Pleurocapsa sp. PCC 7327 U 1 2 7.8 47.6 6100 5796 ATCC; PCC Stanieria cyanosphaera PCC 7437 U 1 5 8.27 45.8 7006 6360 ATCC; PCC Synechococcales Acaryochloris marina MBIC11017 U 1 1 4.89 46.2 4014 3854 NA Chamaesiphon minutus PCC 6605 U 1 0 2.7 55.5 2581 2522 PCC Cyanobium gracile PCC 6307 U 1 1 2.74 55.5 2715 2662 PCC Synechococcus elongatus PCC 6301 U 1 0 2.61 52.4 2944 2892 PCC Synechococcus elongatus PCC 7942 U 1 0 2.51 59.2 2756 2645 ATCC; PCC Synechococcus sp. CC9311 U 1 0 2.23 54.2 2357 2306 NCMA Synechococcus sp. CC9605 U 1 0 3.05 58.5 2942 2862 NCMA Synechococcus sp. CC9902 U 1 0 2.93 60.2 2897 2760 NCMA Synechococcus sp. JA-2-3B'a(2–13) U 1 1 3.72 48.5 3794 3545 NA Synechococcus sp. JA-3-3Ab U 1 6 3.41 49.2 3238 3187 NA Synechococcus sp. PCC 6312 U 1 2 3.58 40.6 3666 3318 ATCC; PCC Synechococcus sp. PCC 7002 U 1 0 2.22 60.8 2581 2533 ATCC; PCC (Continued)

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Table 1. (Continued)

Order Organism Morph. Chr. Pla. Size, MB GC % Genes Proteins BRCs Synechococcus sp. PCC 7502 U 1 0 2.37 60.2 2586 2533 PCC Synechococcus sp. RCC307 U 1 0 2.43 59.4 2581 2519 RCC Synechococcus sp. WH 7803 U 1 0 3.57 47.7 3219 3170 NCMA Synechococcus sp. WH 8102 U 1 4 3.95 47.3 3625 3575 NCMA Synechocystis sp. PCC 6803 U 1 7 3.95 47.3 3610 3561 PCC Synechocystis sp. PCC 6803 U 1 0 3.57 47.7 3218 3169 PCC Synechocystis sp. PCC 6803 U 1 0 3.57 47.7 3217 3168 PCC Synechocystis sp. PCC 6803 substr. GT-I U 1 0 3.57 47.7 3217 3168 PCC Synechocystis sp. PCC 6803 substr. PCC-N U 1 0 2.59 53.9 2525 2476 PCC Synechocystis sp. PCC 6803 substr. PCC-P U 1 0 2.52 53.8 2400 2231 PCC Thermosynechococcus elongatus BP-1 U 1 0 7.75 34.1 5126 4451 NA Thermosynechococcus sp. NK55 U 1 2 6.69 44.4 6033 5752 NA Leptolyngbya sp. PCC 7376 U 1 0 4.99 45.2 4665 4268 ATCC; PCC Pseudanabaena sp. PCC 7367 U 1 5 5.54 36.3 5041 4781 PCC Prochlorococcus marinus str. AS9601 U 1 0 1.67 31.3 1965 1920 NCMA Prochlorococcus marinus str. MIT 9211 U 1 0 1.69 38 1900 1854 NA Prochlorococcus marinus str. MIT 9215 U 1 0 1.74 31.1 2054 1982 NCMA Prochlorococcus marinus str. MIT 9301 U 1 0 1.64 31.3 1962 1906 NCMA Prochlorococcus marinus str. MIT 9303 U 1 0 2.68 50 3136 2997 NCMA Prochlorococcus marinus str. MIT 9312 U 1 0 1.71 31.2 1856 1810 NCMA Prochlorococcus marinus str. MIT 9313 U 1 0 2.41 50.7 2330 2269 NCMA Prochlorococcus marinus str. MIT 9515 U 1 0 1.7 30.8 1964 1905 NCMA Prochlorococcus marinus str. NATL1A U 1 0 1.86 35 2250 2193 NCMA Prochlorococcus marinus str. NATL2A U 1 0 1.84 35.1 2228 2162 NCMA Prochlorococcus marinus subsp. marinus str. CCMP1375 U 1 0 1.75 36.4 1930 1882 NCMA Prochlorococcus marinus subsp. pastoris str. CCMP1986 U 1 0 1.66 30.8 1762 1717 NCMA

The Biological Resource Centers (BRCs) listed (with hyperlinks) includes 1. ATCC (American Type Culture Collection), 2. PCC (Pasteur Culture Collection of Cyanobacteria), 3. NIES (National Institute for Environmental Studies), 4. NCMA (National Center for Marine Algae and Microbiota), 5. RCC (Roscoff Culture Collection) and 6. NA, Not available doi:10.1371/journal.pone.0136262.t001

chromosomes and plasmids. The users have the freedom to restrict their analysis to either chromosomes or plasmids. Furthermore, CKB provides databases that allow users to compare individual organisms, multiple organisms and orders also (Fig 2). As cyanobacteria are prokaryotic photosynthetic organisms, a model prokaryotic genome (E. coli) and a photosynthetic eukaryotic genome (Arabidopsis) are included for advancing comparative analysis. In addition, pattern and fuzzy search tools are available to help in identifying the patterns present in different cyanobacterial genomes. Furthermore, the restriction digestion tool helps to identify restriction sites within the sequences.

Searching and browsing through the database The Cyanobacterial KnowledgeBase consists of information related to 74 fully sequenced cyanobacterial species of seven orders, namely Chroococcales, Chroococcidiopsidales, Gloeobac- teriales, Nostocales, Oscillatoriales, Pleurocapsales and Synechococcales. The browse option helps with orientation and navigation through the species under each order (Fig 3). The species

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Fig 2. CKB BLAST tool. The BLAST analysis tool compares sequence within cyanobacterial species and with E. coli and Arabidopsis. It consists of A, B, C, D and E divisions where A: denotes different programs of BLAST tool, B: the sequence input page, C: option to select the individual or an order wise cyanobacterial dataset, D: choice to choose genomes of 74 cyanobacterial genomes fully or only chromosomes or only plasmids for analysis and E: optionto choose E. coli and /or Arabidopsis. doi:10.1371/journal.pone.0136262.g002

report can be reached from the “Browse by Order” option, which provides brief information about the species, taxonomy, morphological features, genome status, and its genome details. The search tool can also be used to retrieve information related to specific genes, functions, or keywords, etc. An example search result for a query keyword "Chaperone" returned 907 entries (Fig 4)

Proteome profiling The complete gene set of each genome can be accessed under the proteome profiling from the “Species reporter” tool. The table provides a complete gene list with PID gene name (locus_tag), synonym, product name, strand, start and end, length, COG (Clusters of Orthologous Groups) id and GI (Genbank) accession number. Furthermore, the search tool within the table provides an option to search and retrieve the results by specific keyword.

Gene report Information related to each gene is displayed under five sections. The ‘details section’ provides brief information related to the gene, and allows the user to navigate to the nearest genes present on either side of the gene of interest (Fig 5). The ‘sequence feature section’ provides domains, repeats, motif, and binding site information in both graphical and tabular form (Fig 6). The FASTA format of protein and nucleotide sequences are provided at the bottom section with direct links for BLAST analysis. The ‘annotation section’ displays the functions of the gene with gene ontology and UniProt keywords. The last two sections provide links to other external databases and list of homologous proteins respectively.

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Fig 3. Search and browse tool. The CKB search tools allow to search by keywords or accession and browse tool, through which users can peruse to individual organism. doi:10.1371/journal.pone.0136262.g003

Review of other related databases and web-resources The rapidly increasing genomics and proteomics data due to advancements in high throughput data generation has created a need for enhanced data management to empower basic and applied research in cyanobacteria. Many web-based databases and community resources have been created specifically for cyanobacteria to facilitate systems biology analysis using these large data. Table 2 provides the list of databases summarized by Hernández-Prieto et al. [7] which has analytical tools along with the additional web resources and databases that are currently available. The most comprehensive and widely used web based database is CyanoBase [8], which contains currently sequenced and annotated genome sequences, along with gene annotations and information related to various mutations involved in 39 species of cyanobacteria. It also includes tools such as BLAST for genes and genome similarity searches and KazusaMart which

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Fig 4. Search results. Results for keyword "Chaperone" showing 907 entries. doi:10.1371/journal.pone.0136262.g004

can be used to convert identifiers from one format to different formats. CYORF is another community annotated database that provides the open reading frame (ORF) list for approxi- mately 33 genomes along with data from KEGG and DBGET at the GenomeNet, Pfam and Prosite motifs, predicted localization sites and protein 3D structures and tools to search for similar sequences [9]. CyanoBIKE is an instance of BioBike which provides web-based programmable knowledge base for genomic, metabolic and experimental data specifically for cyanobacteria. It has the collection of different datasets along with built-in tools for analysis, which require some basic programming skills for its application [10]. Apart from the above three generalized cyanobacterial databases, there are a few more databases which are developed specifically for a particular species or a group of cyanobacteria, which includes Cyanorak [11], SynechoNET [12] and ProPortal [13]. These are dedicated resources with annotations for orthologous sequences of marine picocyanobacteria, protein- protein interaction data for Synechocystis, and information related Prochlorococcus isolates respectively. Additionally, many specialized databases that are available focusing on specific protein class or property exclusively for cyanobacterial species. It includes cTFbase, a database containing transcription factors [14], CyanoPhyChe, which contains physico-chemical properties of cyanobacterial proteins [15], CyanoClust, which includes homolog groups in cyanobacteria and plastids produced by the program Gclust [16], CyanoEXpress, with curated genome-wide expression data [17] and CyanoLyase, a database of phycobilin lyase sequences, motifs and functions [18].

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Fig 5. Gene report-About section. About section of the gene provides brief information about the gene of interest and genes located either side of the gene. doi:10.1371/journal.pone.0136262.g005

Along with these online databases, CyanoNews [19], Cyanosite [20], CyanoData [21] and CyanoDB [22] are the major web resources that provide the basic information about cyanobacteria, current happenings in cyanobacterial research, the methods used in cyanobacteriology, bibliography archive, research groups involved in cyanobacterial research, etc. that are exten- sively referred by cyanobacteriologists. CKB, the present available database has incorporated all 74 currently fully sequenced genomes of cyanobacteria, including customized tools for inclusive analysis of these genomes. The tool also helps in interpreting newly sequenced genomes by comparing them with the pre- viously annotated cyanobacterial and/or other model organism genomes. The flexibility of defining datasets by either organism or order, or as whole genome or plasmids, helps the user to segregate their search and its results according to their specific needs. An additional signifi- cant characteristic is the inclusion of the model prokaryotic genome (E. coli) and presence of a photosynthetic eukaryotic genome (Arabidopsis), which further assists in comparative sequence analysis thereby making CKB a unique and beneficial resource for cyanobacterial genome analysis.

Future Prospects It is planned to improve and update the content of the database of CKB in the following aspects. First, gene information will be enriched by adding experimentally proven results related to biological functions, expression, and protein-protein interactions by manually

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Fig 6. Sequence features. Graphical and tabular display of sequence features. doi:10.1371/journal.pone.0136262.g006

curating the data from peer reviewed literature. In addition, we intend to include or develop further analysis tools to support the analysis of cyanobacterial genomes. The necessary efforts will also be made to ensure the database as user-friendly and efficient as possible, using the reflection and feedback from users of the first version of CKB to guide our efforts.

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Table 2. List of other databases or web-resources available as at May-2015.

Name Database/Web Details Tools Link to website resource CyanoBase Database Database of genetic data of about 39 species BLAST2, KazusaMart http://genome.microbedb. jp/cyanobase/ CYORF Database Contains ORF list of about 33 species BLAST, FASTA http://cyano.genome.ad.jp/ CyanoBIKE Database A web-based programmable knowledge base for genomic, In built and custom http://biobike.csbc.vcu.edu/ metabolic, and experimental data tools cTFbase Database Database of transcription factors in the cyanobacterial BLAST, Multiple http://bioinformatics.zj.cn/ genomes sequence alignment cTFbase/DatabaseLink. tool php CyanoPhyChe Database Contains data related to physico-chemical properties, structure NA http://bif.uohyd.ac.in/cpc/ and biochemical pathway information of cyanobacterial proteins CyanoClust Database Database of homologous proteins in cyanobacteria and BLAST http://cyanoclust.c.u-tokyo. plastids ac.jp/ CyanoEXpress Database Used for examination and visualisation of gene expression NA http://cyanoexpress. changes for various experimental or genetic manipulations sysbiolab.eu/ from numerous transcriptome studies CyanoLyase Database A manually curated sequence and motif database of BLAST, Pattern http://cyanolyase. phycobilin lyases and related proteins matching tool genouest.org/ (Protomatch) Cyanorak Database Information system of clusters of orthologous sequences from Blast http://www.sb-roscoff.fr/ marine picocyanobacteria cyanorak SynechoNET Database Integrated protein-protein interaction database of NA http://bioportal.kobic.kr/ Synechocystis SynechoNET/ ProPortal Database A resource for integrated systems biology of isolates of NA http://proportal.mit.edu/ Prochlorococcus CyanoNews Web resource Newsletter intended for cyanobacteriologists NA http://www.vcu.edu/ cyanonews/ Cyanosite Web resource A general webserver for cyanobacterial research NA http://www-cyanosite.bio. purdue.edu/ CyanoData Web resource A database for methods for cyanobacterial bloom NA http://www.cyanodata.net/ management faq.php CyanoDB Web resource A taxonomic database of cyanobacterial genera. NA http://www.cyanodb.cz/ doi:10.1371/journal.pone.0136262.t002

Conclusions Here we present CKB as a knowledge database for the cyanobacteriologists. CKB provides access to information related to fully sequenced genomes and can be utilized for analysis and retrieving information. The CKB database website is freely accessible as a web application at: http://nfmc.res.in/ckb.

Materials and Methods Data Collection and Organization The complete genomes of 74 cyanobacteria were downloaded from the NCBI ftp site and their accession numbers are listed in S1 File [23]. Sequence features, annotations, and external links were downloaded from the UniProt database in xml format for each gene [24]. All the downloaded data from NCBI and UniProt databases were converted into csv format and uploaded into a SQL database. The full schema of the database is included as the S1 Fig.

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Web Interface and Application CKB is built on a 64 bit CentOS (version 5) server running WAMPSERVER (V2.2d), which integrates the Apache HTTP Server (V2.2.21) with PHP (V5.3.10) and the MySQL Server (V5.5.20). Complete data related to the sequence and annotations are stored in a MySQL database. The database is designed using PHP, with jQuery JavaScript Library (V1.10), and Cascad- ing Style Sheets (CSS) for the web interface. In addition, a simple gene browser in HTML5 is incorporated into the gene report page, which is provided by Chase Miller [25]. The BLAST 2.2.29+ tool is downloaded from NCBI ftp and pattern and fuzzy search tool and the restriction digestion tools are downloaded from Sequence Manipulation Suite [26–27]. The web server and all information parts of the database are hosted at NFMC portal www.nfmc.res.in.

Supporting Information S1 Fig. Database schema. (TIF) S1 File. List of RefSeq accession numbers. (DOCX)

Acknowledgments The authors sincerely thank the Department of Biotechnology, Government of India, New Delhi for funding the Sub-Distributed Bioinformatics Centre (Grant No. BT/BI/04/038/98)

Author Contributions Conceived and designed the experiments: APP KL. Performed the experiments: APP KL SV SM UL PD. Analyzed the data: APP KL UL PD SG. Contributed reagents/materials/analysis tools: APP KL UL PD ST KA. Wrote the paper: APP KL SV SM UL PD ST KA SG.

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